Dear RDKit community:

I am facing the situation that I would like to attach indices to atoms in a
molecule defined by a substructure. The substitution pattern is of
importance. Therefore I needed to include the wildcards atoms in my
substructure. If I get the atom indices of this substructure, the matched
atoms are still included and will be used for attaching indices (see at the
end of the attached notebook for an example)

I found a solution how to get rid off the non ring atom. That was
straightforward. For the attached atom which is part of another ring I
needed to do something differently. I determined the atom indices in each
ring with GetRingInfo and then I determined which of these rings is part of
the tuple of the atom indices of the pattern. Once determined I can do what
I need.

The question to you is: Is there another more elegant way of doing it? May
be I missed something from the python API?

I would appreciate any input.


Attachment: AtomMapping.ipynb
Description: Binary data

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